Estimates of regional infectivity of COVID-19 in the United Kingdom following imposition of social distancing measures

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reproduction number has become an essential parameter for monitoring disease transmission across settings and guiding interventions. The UK published weekly estimates of the reproduction number in the UK starting in May 2020 which are formed from multiple independent estimates. In this paper, we describe methods used to estimate the time-varying SARS-CoV-2 reproduction number for the UK. We used multiple data sources and estimated a serial interval distribution from published studies. We describe regional variability and how estimates evolved during the early phases of the outbreak, until the relaxing of social distancing measures began to be introduced in early July. Our analysis is able to guide localized control and provides a longitudinal example of applying these methods over long timescales. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.

Keywords: COVID-19; SARS-CoV-2; regional variation; reproduction number.

Figure 1.

Timeline of cases and estimates of R_t based on cases reported by PHE and NHS laboratories (green), deaths reported in NHS trusts (red) and best available data for hospital admissions (blue). (a) Number of cases (Pillar 1), deaths and admissions per million; (b) estimates of R_t. Red points are either missing values or identified as anomalies and replacements imputed.

Figure 2.

The median value of R_t and 95% confidence intervals for the individual countries in the UK, based on cases, deaths and hospital admissions, and a 28-day rolling window. For each data source, red points represent data points that were missing and have been imputed.

Figure 3.

The median value of R_t and 95% confidence intervals for the sub-national regions of NHS England, based on cases, deaths and hospital admissions, and a 7-day rolling window.

Figure 4.

The difference of R_t estimates for NHS regions and baseline R_t estimates for England, based on cases, deaths and hospital admissions, and a 28-day rolling window.